[gmx-users] Hi,David and everyone insterests in itp

[K.A. Feenstra]

nanyu101 wrote:
> Hi,
>   I am sorry to bother you alone.But there are some problems puzzled me very much.
 > I do know that I can create a itp file for a single molecule,such as Urea, TFE and
 > DPPC.In my system, I do a polyester in bilayer.because it is a chain as protein and
 > DNA,what I should do if I want to create itp file for this polyester?Should I create
 > three itp files,one is first monomer;second is the middle monomers;the last is the
 >  last monomer.If so,what I should do because the molecule is connected by monomer.
 > There is a little different from a single molecule such as DPPC and Urea.Or I have
 > some other way to resolve it.If so,should I create a termini database for it?
 > How can I manage it?

You already have an .rtp file (you said that previously). Run your .pdb file through
pdb2gmx using your .rtp file. pdb2gmx will generate a .top file for your polymer.
The residue names for first and last terminal and for middle residues must match
between the .pdb file and the .rtp file.

>   I have checked gmx-users maillist, there is nobody who ever met this problem.
 > So I have to ask for you help.I hope you can give me some assistant.

I'm certain that similar issues have been discussed at several occasions... ;-/


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
|________|___________________________________________________________|